Nail their hands to their guns, beat them, force them to seek penance through suffering, then let them go when they reach their destination.
If they weren't so important she should kill them outright, for not only the theft but the waste of sacred ammunition and the serious danger their transgression put - not just her, but the interest of the Emperor - in.
Another idea would be to force each of them to turn over something of personal meaning and value - which she might either keep or destroy right in front of them.
Removing a hand, then later replacing it so they aren't actually inconvenienced by it, seems rather pointless - the punishment only serves a purpose if it teaches them not to repeat the behavior.

) It made life interesting, because we were declared excommunicated by the local Inquisitor, not the Inquisitor we actually reported to who was on the other side of the Calixis sector, so we ignored the excommunicatus order and kept following the orders from our Inquisitor, but it did make everything extremely difficult because of course the other Inquisitor started hunting us down and we no longer had any authority with local officials. It was much worse than any corporal punishment he could have dealt out. 